For nearly the entire game, defending Atlantic 10 Tournament champion Duquesne was in control of its second-round matchup Thursday against longtime rival St. Bonaventure.

Then, the Dukes lost it.

Lajae Jones and Melvin Council Jr. scored 18 points apiece, No. 8 seed St. Bonaventure used a 13-1 run in the final 3 minutes, 47 seconds and the Bonnies, trailing No. 9 Duquesne for nearly the entire way, came away with a 64-59 victory at Capital One Arena in Washington, D.C.

“We just said, ‘Keep playing, keep playing,’ and that’s what we did,” Council said in a postgame interview on USA Network.

St. Bonaventure (22-10), which led for just 2:04 and fell behind by as many as 13 points in the second half, advanced to the quarterfinals against top-seeded VCU at 11:30 a.m. Friday.

In the 137th meeting between the schools — the most games played against Duquesne by an opponent — the phrase, “Excellent team defense,” was heard early and often.

And, for much of the game, the Dukes’ defense was superb.

But St. Bonaventure, which mostly goes with a thin seven-player rotation, got hot down the stretch.

Council’s jumper with 2:19 to go pulled St. Bonaventure even at 58-58, bringing the Bonnies back from a 48-35 deficit at the 12:34 mark.

He sank a pair of free throws less than a minute later, and Duquesne’s lead was gone for good.

Maximus Edwards led the Dukes (13-19) with 18 points. Matus Hronsky added 11 and Tre Dinkins III chipped in 10.

Jakub Necas’ 10 rebounds paced Duquesne’s 40-30 edge on the glass, but 18 turnovers — a number of them late — contributed to their collapse.

Snubbed in voting for the league’s postseason awards, Duquesne’s depth, balance and defense was on display at a high level for much of the time.

But it was St. Bonaventure’s compact and cohesive lineup that allowed the Bonnies to prevail.

Duquesne took its first double-digit lead when Edwards drained a 3-pointer with a hand in his face, giving the Dukes a 43-32 cushion with 14:25 left.

Edwards followed with a dunk to extend the margin to 13 points, and it returned to a 13-point advantage after Edwards traded 3-point shots with St. Bonaventure’s Jonah Hinson at the 12:34 mark.

After that, the Bonnies chipped away and finally took the lead late and held on.

Duquesne failed to make a field goal in the final 4:16.

This story will be updated.